The antimalarial chloroquine concentrates in the acid vesicles of Plasmodium falciparum partially as a result of its properties as a weak base. Chloroquine-resistant parasites accumulate less drug than sensitive parasites. A simple hypothesis is that the intravacuolar pH of resistant strains is higher than that for sensitive strains, as a consequence of a weakened proton pump in the vacuoles of resistant strains, thereby explaining the resistance mechanism. We have attempted to test this hypothesis by the use of bafilomycin A1, a specific inhibitor of vacuolar proton pumping ATPase systems in plant cells, animal cells and microorganisms. Bafilomycin A1 significantly reduces uptake of [3H]chloroquine into both chloroquine-sensitive and -resistant strains of P. falciparum, at concentrations of inhibitor which have no antimalarial effect. Additionally, chloroquine-resistant strains of P. falciparum are more sensitive to bafilomycin A1 than chloroquine-sensitive strains. The use of bafilomycin A1 in combination with chloroquine in the standard in vitro sensitivity assay, produced an apparent reduction in sensitivity of both strains to chloroquine. The reported data support the hypothesis that chloroquine resistance in P. falciparum is associated with increased vacuolar pH, possibly due to a weakened vacuolar proton pumping ATPase.